Contacts of the helix formed by residues 96 - 104 (chain D) in PDB entry 5X11
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 96 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33C PHE* 3.0 30.8 + - + +
34C TRP* 4.1 1.7 - - - -
94C VAL* 6.4 0.2 - - + -
160C LYS* 5.1 0.7 + - - -
164C ARG* 5.4 1.8 - - - +
94D VAL 4.2 5.4 - - - +
95D LYS* 1.3 76.2 - - - +
97D GLU* 1.3 65.0 + - - +
98D PHE* 3.0 16.3 + - - +
99D MET* 3.0 25.2 + - + +
100D LEU* 3.4 7.6 + - - +
124D ARG* 4.7 6.5 + - - -
168D TYR* 2.5 40.2 + - - -
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Residues in contact with GLU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C VAL* 3.8 38.2 - - + +
34C TRP* 4.2 15.2 - - + -
83C TRP* 3.2 31.7 + - + -
88C GLN* 4.6 20.3 - - - +
96D ASP* 1.3 73.2 + - - +
98D PHE* 1.3 62.0 + - - +
100D LEU* 3.2 21.2 - - - +
101D LYS* 3.3 15.3 + - - +
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Residues in contact with PHE 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D ASP* 3.0 11.6 + - - +
97D GLU* 1.3 78.9 - - - +
99D MET* 1.3 64.3 + - - +
101D LYS* 3.0 19.4 + - + +
102D ALA* 2.9 26.5 + - + -
116D LEU* 3.8 26.9 - - + -
117D PHE* 3.9 39.5 - + - -
120D GLN* 3.3 50.0 - - + +
124D ARG* 5.6 0.2 - - - +
168D TYR* 3.7 17.0 - + - +
171D TRP* 4.2 6.5 - + - -
172D LEU* 3.9 17.0 - - + -
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Residues in contact with MET 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LEU* 5.6 0.4 - - - -
33C PHE* 3.5 38.6 - - + -
156C LEU 3.7 13.2 - - - +
157C VAL* 3.8 21.5 - - + +
160C LYS* 3.6 33.7 - - + -
96D ASP* 3.0 25.8 + - - +
98D PHE* 1.3 80.6 - - - +
100D LEU* 1.3 66.0 + - - +
102D ALA* 3.3 21.9 + - + +
103D TYR* 2.9 22.9 + - - +
168D TYR* 4.2 2.7 - - - -
171D TRP* 3.7 20.6 - - + -
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Residues in contact with LEU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C VAL* 3.7 31.0 - - + +
7C ALA* 4.0 20.4 - - + -
26C PHE* 4.9 0.2 - - + -
30C LEU* 3.5 34.1 - - + -
33C PHE* 5.1 1.4 - - - +
34C TRP* 3.9 27.6 - - + -
83C TRP* 4.3 10.5 - - + -
96D ASP 3.4 5.2 + - - +
97D GLU* 3.2 12.7 + - - +
99D MET* 1.3 77.0 - - - +
101D LYS* 1.3 63.0 + - - +
103D TYR* 3.2 15.0 + - - +
104D PHE* 3.3 37.6 + - + -
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Residues in contact with LYS 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C TRP* 2.8 66.6 + - + +
84C LEU* 3.7 30.4 + - + +
86C ARG* 2.8 24.0 + - - +
88C GLN* 4.8 10.4 - - - +
97D GLU* 3.3 14.1 + - - +
98D PHE* 3.0 17.4 + - + +
100D LEU* 1.3 78.7 - - - +
102D ALA* 1.3 63.8 + - - +
104D PHE* 3.0 15.1 + - - +
105D ILE* 3.4 9.0 + - - +
108D LEU* 5.4 1.2 - - - +
116D LEU* 4.2 27.6 - - + +
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Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C GLY* 3.9 0.3 - - - -
156C LEU* 3.5 23.5 - - + +
98D PHE* 2.9 13.3 + - + +
99D MET* 3.5 31.6 - - + +
100D LEU 3.3 0.2 - - - -
101D LYS* 1.3 76.0 - - - +
103D TYR* 1.3 63.7 + - - +
105D ILE* 3.0 27.9 + - - +
116D LEU* 5.5 0.4 - - - +
117D PHE* 4.1 21.3 - - + -
171D TRP* 4.6 0.9 - - + -
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Residues in contact with TYR 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 4.0 22.0 - - + -
13C ARG* 3.4 24.6 + - - -
25C TYR* 3.9 17.5 - - - -
29C GLU* 2.7 41.6 + - + -
30C LEU* 3.6 28.8 - - + +
153C GLY* 3.5 23.5 - - - -
154C HIS* 4.1 11.6 + - + -
157C VAL* 3.6 26.8 - - + +
99D MET 2.9 13.9 + - - +
100D LEU 3.2 10.1 + - - +
102D ALA* 1.3 75.2 - - - +
104D PHE* 1.3 75.7 + + - +
105D ILE* 3.4 3.6 + - - +
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Residues in contact with PHE 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C TYR 3.5 18.6 - - - -
7C ALA* 3.4 24.2 - - - -
10C GLY* 3.3 34.1 - - - -
11C LEU* 3.4 10.8 - - + -
13C ARG* 3.7 20.3 + - - +
30C LEU* 4.9 0.9 - - + -
80C LEU* 4.5 1.8 - - + -
83C TRP* 4.0 18.6 - + - -
84C LEU* 4.0 14.4 - - + +
100D LEU* 3.3 37.7 - - + -
101D LYS 3.0 10.6 + - - +
103D TYR* 1.3 95.4 - + - +
105D ILE* 1.3 53.5 + - - +
106D SER 2.8 15.6 + - - -
107D SER* 2.9 19.1 + - - -
108D LEU* 5.4 0.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il